Chromosome translocations have been correlated with multiple diverse cancers including leukemia, lymphoma, breast cancer, renal cancer, peripheral neuroepithelioma, synovial carcinoma, and ganglioneuroblastomas (see, e.g., Onida et al., Cancer 95(8):1673–84 (2002); Million et al., Blood 99(12):4568–77 (2002); Popovici et al., Genes Chromosomes Cancer 35(3):204–18 (2002); Bodmer et al., Cancer Genet Cytogenet. 136(2):95–100 (2002); Podolski et al., J Hum Genet. 46(12):685–93 (2001); Dai et al., Zhonghua Yi Xue Za Zhi (Taipei) 65(6):293–7 (2002); Van Roy et al, Genes Chromosomes Cancer 35(2):113–20 (2002); Sossey-Alaoui et al., Oncogene 21(38):5967–74 (2002)). For example, since the discovery of the BCR-ABL fusion gene, more than 50 different consistently occurring translocations associated with leukemic cells have been identified (Pallisgaard et al., Blood 92:574–588 (1998)). These chromosomal structural rearrangements may directly or indirectly alter the activities of cellular proto-oncogenes, especially transcription factors, resulting in disturbance of the normal programs of cell proliferation, differentiation, and apoptosis (Look, Science 278:1059–1064 (1997)). These genes can play key roles in the development and function of cells, and their alteration may act in concert with other genetic changes in a multiple step pathway to result in oncogenic transformation.
For example, chromosome translocations are found in up to 65% of the acute leukemias, and the nature of these translocations can delineate patients with a defined prognosis. Clinical studies have shown that many of these translocations are specific for particular subtypes of leukemias, so that chromosome rearrangements can also be used for risk group classification in acute lymphoblastic leukemia and acute myeloid leukemia. This has greatly improved treatment of the acute leukemias by using a protocol tailored to the risk of relapse in discrete subgroups instead of uniform strategies for all patients ((Look, 1997, supra). Although routine clinical parameters, such as age, white blood cell count, and blast cell immunophenotype, provide useful criteria for risk assessment, the determination of chromosome rearrangement offers much more valuable prognosis information for cancer patients.
A number of assays have been developed for the determination of chromosome arrangement. For example, cytogenetic assays such as FISH (fluorescence in situ hybridization) are useful methods to detect chromosome translocations and can be valuable tools for cancer prognosis. However, cytogenetic assays are time- and labor-intensive, and require sufficient metaphase cells, which are difficult to obtain for some patient samples (Pallisgaard et al., 1998, supra and Popescu et al., Cancer Genetics and Cytogenetics 93:10–21 (1997)). Reverse transcriptase (RT)-polymerase chain reaction (PCR)-based assays to identify chromosome translocations have also been developed. RT-PCR based assays are much more sensitive than cytogenetic assays and can be performed on resting cells. However, for an unequivocal molecular diagnosis, RT-PCR-based methods must be augmented with hybridization probes or direct sequencing, adding to the time, cost, and technical complexity of the method. Thus, for early molecular diagnostics applications, especially initial characterization of patient samples, new tools are needed.
There has been increasing interest in the use of microparticle arrays for high throughput screening to detect genetic abnormalities, including chromosome translocations. The concept of using microspheres and flow cytometry to perform multiplexed assays was initially proposed by Horan and Wheeless, Science 198(4313):149–57 (1977), using different sized microspheres, and further developed recently using different colored microspheres (Fulton et al., Clinical Chemistry 43:1749–1756 (1997)). The use of microparticle arrays has been described for immunoassays, single nucleotide polymorphism (SNP) (see, e.g., U.S. Pat. No. 6,287,766), genotyping, bacterial signature detection, and detection of DNA or RNA viruses (Fulton et al., 1997, supra; Cai et al., Genomics 66:135–143 (2000); Nolan et al. 47th Annual Meeting of the American Society of Human Genetics, Oct. 28-Nov. 1, 1997 Baltimore Md.; Iannone et al., Cytometry 39:131–140 (2000); Vignali, J. Immunological Methods 243:243–255 (2000); Armstrong et al, Cytometry 40:102–108 (2000); and Defoort et al., J. Clinical Microbiology 38:1066–1071(2000)).
There is a need in the art for methods of identifying chromosome translocations and methods for diagnosing cancer. The present invention addresses this need.